Automatic thresholding of each image in a time series and z-stack based on image intensity properties and accounting for bleaching.

http://dl.dropbox.com/u/1236815/cell_img.jpg

I have a series of images of cells taken in time series and z-stacks. I'm trying to threshold for the cell unfortunately there is bleaching and i cant use the same value through the whole series. I tried using linspace to generate threshold values based on the first and last images which i found by trial and error. However the cell seems to be bleaching in some kind of exponential and the linspace obviously does not account for that. I have also tried using stdfilt and medianfilt2 to reduce the noise, but this doesnt seem to help either.

Is there anyway that i can generate threshold values for the cell based on the intensity? the link above is among the most bleached of images I cannot use mat2gray because its also a z-stack and i only want those images that are actually in focus.

thanks for your help!

Answer 1

[Image Analyst]

60 is not that many. Why not just do it interactively with my thresholding app? http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862

[gargoyle]

60 is for one cell. I have a lot of them not to mention future experiments... although i will have a look see at your program.

Answer 2

[gargoyle]

for now i have used spline interpolation on empirically determined values for 4 out of 60 timepoints and it works quite well... however if anyone does know any better method to glean signal i would love to know